Operating the shruti petti with the feet and legs is nothing new for flautists and has nothing to do with Mali sir's "torment" or "antics". The point is that no sensitive flautist likes to play without shruti and there's not always somebody to operate it. Those were the pre-electronic days.
My flute guru T S Sankaran sir, Mali's disciple, used to do it and apparently taught it to all his students prior to the advent of the electronic shruti box (which is when I went to him
). Even after the advent of the electronic box in the late 80's Sankaran sir used to practice with the acoustic shruti box, operating it with his feet and legs. It can be done sitting cross legged and wrapping one leg around the shruti box and buttressing it with the other leg.
The intonation of the flute is a partial function of the blowing. Typically, when you're tired and blow with less gusto your pitch falls ("theychal") a bit on all notes. The problem is exacerbated when you "over blow", i.e., attain the higher pitches by blowing harder for the same fingering. It becomes particuarly acute at mel sa and above and everybody, even Mali sir, occassionally "falls short" at the mel Sa. Sometimes flutists perform entire concerts with slight "theychal" at mel Sa and above, kind of like GNB in his later days. This is also a function of the instrument itself and the position of the blow hole from the blocked end - hence it is that flautists must select their instruments very carefully. Also, the higher the pitch of the flute, the more discernible is pitch misalignment. Hence you'll never find Hariprasad Chaurasia "falling short" in a readily discernible way. This is because he operates at the lower D key, an octave and a half lower than mali sir's G flute and of course he is inherently pitch sensitive. But I would wager that even Chaurasia would have some occassional "theychal" if he played the higher G flute.
Lastly, it is more wholesome and satisfying from a shruti perspective to play wind instruments like flute and nagasvaram to the accompaniment of the shruti petti rather than the tambura.